I guess there is a number of reasons... One might be simply be lazy (hey it does take a couple of seconds to put it on ). Another would be that the average bokken has a rather short handle and if you don't use the tsuba you can extend your grip a little up the sword, thereby gaining better control. I know this is not in compliance with 'realistic practice', but in paired practice I prefer safety to realism.
The way I see it, there is no use in putting the tsuba on the bokken, as it has no or very little practical use when it comes to protection. With my limited knowledge of sword-work I would never rely on the tsuba to protect my hands, instead the protection should be to move out of the line of the attack and take the center. In 'real life' this should be the same. I would be very scared if the tsuba was the only thing keeping my opponents sword from cutting my hand. It is not large enough nor strong enough to be a reliable 'safety-valve' and I don't think the blocking way to use the sword is the kind of technique one should practice.
I have had some experience with both Seitei-iaido, Aiki-toho, Kendo, Aiki-ken tai jo and Aiki-ken tai ken, and in neither of these arts have I experienced any technique relying on the tsuba for anything else than a means to either keep the sword in the scabbard (left hands thumb controls it) or getting the sword out of the scabbard quickly (left hand thumb pushes on the side of the tsuba to get loosen the sword from the firm grip of the scabbard).
Finally when using the bokken while practicing aikido the tsuba could (in theory) in some situations either scratch uke or put pressure on ukes wrist, so to prevent to add discomfort to uke I don't put it on.

In conclusion: I have very little reason NOT to use a tsuba, and slightly less reason to use it - so I don't. (However what put's me over the top might be the 'when in Rome' factor )